#Triangular Distribution Monte Carlo for Rapfish

# 2012-04-15 Divya Varkey Created

#to be obtained from site

nsim=100
num_fish=53
anchor_files=c('anchors4.csv','anchors5.csv','anchors6.csv','anchors7.csv','anchors
8.csv','anchors9.csv','anchors10.csv','anchors11.csv','anchors12.csv')
filenames=c('CCRF_Field1.csv','CCRF_Field2.csv','CCRF_Field3.csv','CCRF_Field4.csv'
,'CCRF_Field5.csv','CCRF_Field6.csv')

###########generated here
nfield=length(filenames)
discipline.names =strsplit(filenames, ".csv")
images_tri=paste(discipline.names,"_Triangle_MC",".jpg",sep="")
res_tri=paste("MC_Triangle_",discipline.names,".csv",sep="")

source("rapfish_functions.R")
source("functiontri.r")

L1=num_fish+1
L2=L1+num_fish-1

U1=L2+1
U2=U1+num_fish-1

####################TRIANGULAR MC
Trig_RapfishMC<-function(fisheries.all,num_fish,nsim)
{
n_att=ncol(fisheries.all)
fisheries.dat=fisheries.all[1:num_fish,]
lb=fisheries.all[L1:L2,]
ub=fisheries.all[U1:U2,]

anchors=loaddata(anchor_files[n_att-3])
colnames(anchors)<-colnames(fisheries.all)

mc_init=array(data=0,dim=c(num_fish,n_att,nsim))
for(j in 1:num_fish) {
for(k in 1:n_att) {
mc_init[j,k,]=rtri(nsim,lb[j,k],ub[j,k],fisheries.dat[j,k])
}
}

fish_mc_res=array(data=0,dim=c(num_fish+nrow(anchors),2,nsim))
for(m in 1:nsim) {
fish_mc.dat=round(mc_init[1:num_fish,1:n_att,m],1)
colnames(fish_mc.dat)<-colnames(fisheries.all)
fish_mc.raw=rbind(anchors,fish_mc.dat)
fish_mc.scaled = mdscale(fish_mc.raw)
fish_mc_res[,,m]=fish_mc.scaled
}

output<-list()
output$mc_init=mc_init
output$fish_mc_res=fish_mc_res
return(output)
}
 ###############################MC PLOTS

for(i in 1:nfield) {

fisheries.all = loaddata(filenames[i])
tt=Trig_RapfishMC(fisheries.all,num_fish,nsim)
n_att=ncol(fisheries.all)
fisheries.dat=fisheries.all[1:num_fish,]

anchors=loaddata(anchor_files[n_att-3])
colnames(anchors)<-colnames(fisheries.all)

fisheries.raw=rbind(anchors,fisheries.dat)
fisheries.scaled = mdscale(fisheries.raw)

n_an=nrow(anchors)
plot1=n_an+1
plot2=n_an+num_fish
cols=rainbow(num_fish,start=0, end=.7)

jpeg(filename=images_tri[i],width=20,height=16,units="cm",res=500)

Res=ifelse(nfield>30,RAPplot1(fisheries.scaled,num_fish,n_an),RAPplot2(fisheries.sc
aled,num_fish,n_an))

mtext(side=3, line=1, "Triangular MC",adj=1)

mtext(side=3, line=1, discipline.names[i],adj=0)

for(m in 1:nsim) {
mcplot=tt$fish_mc_res[plot1:plot2,,m]
mcplot = mcplot[order(fisheries.scaled[plot1:plot2,1]),]
points(mcplot,xlab="",ylab="",col=cols,pch='.')
}

dev.off()

mc_summ=matrix(data=0,nrow=num_fish,ncol=12)
s_mcres=tt$fish_mc_res[plot1:plot2,,]

for(fs in 1:num_fish) {
xx=round(quantile(s_mcres[fs,1,],probs=c(0.5,0.25,0.75,0.025,0.975)),4)
yy=round(quantile(s_mcres[fs,2,],probs=c(0.5,0.25,0.75,0.025,0.975)),4)

mc_summ[fs,2:6]=xx
mc_summ[fs,8:12]=yy
}

mc_summ[,1]=round(fisheries.scaled[plot1:plot2,1],4)
mc_summ[,5]=round(fisheries.scaled[plot1:plot2,2],4)
colnames(mc_summ)<-
c("X_Scores","Median","25%","75%","2.5%","97.5%","Y_Scores","Median","25%","75%","2
.5%","97.5%")
rownames(mc_summ)<-rownames(fisheries.dat)
write.csv(mc_summ,res_tri[i])
}